Fumarase: A Mitochondrial Metabolic Enzyme and a Cytosolic/Nuclear Component of the DNA Damage Response

Yogev, Ohad; Yogev, Orli; Singer, Esti; Shaulian, Eitan; Goldberg, Michal; Fox, Thomas D.; Pines, Ophry

doi:10.1371/journal.pbio.1000328

Cited by 189 publications

(205 citation statements)

References 36 publications

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“…This function could be limited to simple regulation of enzymatic activity, or it could involve a second unrelated process. Dual functions of several metabolic enzymes have recently been reported (27)(28)(29)(30), and in particular, the human fumarate hydratase has been implicated in the DNA damage response (31)(32)(33). The existence of these dual functions of metabolic enzymes suggests that potential biological functions of this allosteric site deserve additional exploration.…”

Section: Discussionmentioning

confidence: 99%

Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site

Kasbekar

Fischer

Mott

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Enzymes in essential metabolic pathways are attractive targets for the treatment of bacterial diseases, but in many cases, the presence of homologous human enzymes makes them impractical candidates for drug development. Fumarate hydratase, an essential enzyme in the tricarboxylic acid (TCA) cycle, has been identified as one such potential therapeutic target in tuberculosis. We report the discovery of the first small molecule inhibitor, to our knowledge, of the Mycobacterium tuberculosis fumarate hydratase. A crystal structure at 2.0-Å resolution of the compound in complex with the protein establishes the existence of a previously unidentified allosteric regulatory site. This allosteric site allows for selective inhibition with respect to the homologous human enzyme. We observe a unique binding mode in which two inhibitor molecules interact within the allosteric site, driving significant conformational changes that preclude simultaneous substrate and inhibitor binding. Our results demonstrate the selective inhibition of a highly conserved metabolic enzyme that contains identical active site residues in both the host and the pathogen. Because the tricarboxylic acid (TCA) cycle connects many pathways of cellular metabolism, preventing the function of this cycle through enzyme inhibition is an attractive strategy for targeting infectious agents (1). In Mycobacterium tuberculosis, experimental evidence (2) has suggested that fumarate hydratase, the essential enzyme responsible for the reversible conversion of fumarate to (L)-malate, is a vulnerable target. This vulnerability is in part due to the fact that, unlike other bacteria (such as Escherichia coli), M. tuberculosis expresses only one enzyme that performs this function (3). In addition to its role in metabolism under aerobic conditions, fumarate hydratase has also garnered interest because of the discovery of a flux toward the reverse TCA cycle under hypoxic conditions in nonreplicating M. tuberculosis (2, 4, 5). However, despite these discoveries, no small molecule inhibitor of the M. tuberculosis fumarate hydratase has been reported. The discovery of such an inhibitor would provide an important tool to begin probing the role of the TCA cycle in both actively replicating and nonreplicating bacteria.From the standpoint of drug development, however, targeting the M. tuberculosis fumarate hydratase poses a significant challenge, because the protein is highly evolutionarily conserved. In particular, the human and M. tuberculosis homologs share identical active site residues as well as 53% overall sequence identity (6, 7). Both homologs form a stable homotetramer containing four active sites, and every active site is composed of residues from three enzyme subunits. Each dumbbell-shaped subunit within the tetramer contains three domains: an N-terminal domain, a central domain, and a C-terminal domain (8-10). The N-and C-terminal domains are predominantly α-helical and linked by the central domain that consists of five tightly packed helices. The central domains of ...

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Section: Discussionmentioning

confidence: 99%

Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site

Kasbekar

Fischer

Mott

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Mutants in the gluconeogenesis enzyme Fbp1, for example, are resistant to MMS-induced DNA damage, potentially through a mechanism tied to metabolic flux (Kitanovic and Wolfl 2006). Another parallel for Lys20, in terms of DNA repair, may be the Krebs cycle enzyme fumarase, which was discovered recently to have DNA repair functions dependent on its catalytic activity (Yogev et al 2010). Checkpoint activation is impaired in fumarase mutants, and mutants are sensitive to DNA damage, in contrast to lys20D.…”

Section: Noncanonical Hats and Metabolic Enzymes In The Nucleusmentioning

confidence: 99%

Homocitrate synthase connects amino acid metabolism to chromatin functions through Esa1 and DNA damage

Scott¹,

Pillus²

2010

Genes Dev.

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The enzyme homocitrate synthase (HCS) catalyzes the first step in lysine biosynthesis, and early biochemical data placed it in the cytoplasm or mitochondria, where most amino acid synthesis occurs. It was therefore surprising when refined fractionation techniques and specific immunoreagents clearly demonstrated its localization to the nucleus. These observations raised the question of whether HCS had a function within the nucleus independent of lysine synthesis. We demonstrate that HCS encoded by LYS20 in yeast is linked to the key process of DNA damage repair through the essential MYST family histone acetyltransferase Esa1 and the H2A.Z histone variant. This discovery indicates that HCS has a role in addition to amino acid synthesis, and that it functions in nuclear activities involving chromatin regulation that are distinct from its previously established role in lysine biosynthesis. The chromatin-linked roles are dependent on nuclear localization of Lys20, but are independent of HCS catalytic activity. Thus, Lys20 appears to have evolved as a bifunctional protein that connects cellular metabolism with chromatin functions.[Keywords: Lysine; histone; DNA damage; yeast; Htz1; bifunctional protein] Supplemental material is available at http://www.genesdev.org.

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“…The HIF increased the expressions of angiogenesisregulated genes, such as VEGF, which led to high microvessel density and tumorigenesis. Therefore, FH functions as a tumor suppressor (Sudarshan et al, 2009;Yogev et al, 2010). Since no other enzyme of the Krebs cycle was detected with a significantly different expression in this study, whether or not the increased expression of FH correlated with the migration and invasive potential of ovarian cancer cells was unknown.…”

Section: Discussionmentioning

confidence: 80%

Up-regulation of mitochondrial antioxidation signals in ovarian cancer cells with aggressive biologic behavior

Wang

Dong

Cui

et al. 2011

J. Zhejiang Univ. Sci. B

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Abstract:Objective: Recently, a high frequency of mutations in mitochondrial DNA (mtDNA) has been detected in ovarian cancer. To explore the alterations of proteins in mitochondria in ovarian cancer, a pair of human ovarian carcinoma cell lines (SKOV3/SKOV3.ip1) with different metastatic potentials was examined. Methods: Cancer cells SKOV3.ip1 were derived from the ascitic tumor cells of nude mice bearing a tumor of ovarian cancer cells SKOV3. SKOV3.ip1 exhibited a higher degree of migration potential than its paired cell line SKOV3. The proteins in the mitochondria of these two cells were isolated and separated by 2-D gel electrophoresis. The differently expressed proteins were extracted and identified using matrix assisted laser desorption ionisation/time-of-flight/time-of-flight (MALDI-TOF/TOF), and finally a selected protein candidate was further investigated by immunohistochemistry (IHC) method in nude mice bearing tumor tissues of these two cells. Results: A total of 35 spots with different expressions were identified between the two cells using 2D-polyacrylamide gel electrophoresis (PAGE) approach. Among them, 17 spots were detected only in either SKOV3 or SKOV3.ip1 cells. Eighteen spots expressed different levels, with as much as a three-fold difference between the two cells. Twenty spots were analyzed using MALDI-TOF/TOF, and 11 of them were identified successfully; four were known to be located in mitochondria, including superoxide dismutase 2 (SOD2), fumarate hydratase (FH), mitochondrial ribosomal protein L38 (MRPL38), and mRNA turnover 4 homolog (MRTO4). An increased staining of SOD2 was observed in SKOV3.ip1 over that of SKOV3 in IHC analysis. Conclusions: Our results indicate that the enhanced antioxidation and metabolic potentials of ovarian cancer cells might contribute to their aggressive and metastatic behaviors. The underlying mechanism warrants further study.

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Fumarase: A Mitochondrial Metabolic Enzyme and a Cytosolic/Nuclear Component of the DNA Damage Response

Abstract: Upon DNA damage, a cytosolic form of the mitochondrial enzyme fumarase moves into the nucleus where, by virtue of its enzymatic activity, it participates in the cell's response to DNA damage. This potentially explains its known role as a tumor suppressor.

Cited by 189 publications

References 36 publications

Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site

Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site

Homocitrate synthase connects amino acid metabolism to chromatin functions through Esa1 and DNA damage

Up-regulation of mitochondrial antioxidation signals in ovarian cancer cells with aggressive biologic behavior

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